GLP-1 Glyco-Masking Program

Full results of the 5-agent, 5-phase in silico pipeline. Objective: design GLP-1 analogs that preserve ≥70% receptor activation while reducing early receptor accessibility (nausea proxy) via covalent glycan masking and a cleavable linker.

Phase Gate Results

GatePhaseCriterionInPassKeptNotes
G1 ✓Masking Feasibility≥50% SASA suppression, binding not zeroed502610Only biantennary-class glycans pass; monosaccharide / O-linked core-1 serve as negative controls.
G2 ✓Linker Timingt½ ∈ [1–6 h], delayed activation confirmed20165Simple esters (t½ <1 h) eliminated. Hydrazone borderline (t½ 6.5 h). PABC/disulfide/carbonate pass.
G3 ✓Receptor Activation≥70% predicted efficacy, unmasked binding ≥0.6050483Y25W aromatic gain + A8T DPP-4 resistance drive top candidates above 100% efficacy.
G4 ✓Temporal PK ModelLate/early ratio ≥3× baseline (~3.15)333All three achieve late/early ratio of 5.58× vs baseline 1.05. All pass.

Synthesis-Ready Candidates

Rank 1GLP1-GM-F54D54Synthesize First
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Sequence & Mutations

HTEGTFTSDVSAYLQGQAWKEAIAWLVKGR
  • A8TCreates Thr anchor for O-glycosylation; DPP-4 resistance
  • S18AHelix stabilisation; additional DPP-4 resistance
  • E21QNeutral amide; improved helical propensity
  • Y25WTrp aromatic stacking with GLP-1R ECD; binding gain
  • G28AHelix C-cap methylation; mild stability gain

Design

Glycan:
Biantennary sialylated N-glycan (SA₂Gal₂GlcNAc₂Man₃GlcNAc₂)
Position:
Glu9 (O-linked via A8T→Thr anchor)
Linker:
Cathepsin B-cleavable GFLG tetrapeptide
t½:
5.72 h
SASA supp.
82.5%
Efficacy
102.7%
Late/Early
5.58×
Score
0.7940
MW (est.)
5762 Da

Activation Profile

0%25%50%75%100%0h0.5h1h2h4h8h12h24hBaseline GLP-1Glyco-masked

Highest composite score driven by Y25W receptor gain (+7% binding) and strongest masking. Cathepsin B cleavage in endosomal compartment ensures spatially confined, delayed activation.

Rank 2GLP1-GM-942303
View in Mol*

Sequence & Mutations

HTEGTFTSDVSAYLQGQAWKEFIAWLVKGR
  • A8TO-glycosylation anchor; DPP-4 resistance
  • S18AHelix stabilisation
  • E21QNeutral amide; improved helical propensity
  • Y25WTrp aromatic contact with GLP-1R

Design

Glycan:
Biantennary sialylated N-glycan
Position:
Glu9 (O-linked via A8T→Thr anchor)
Linker:
Cathepsin B-cleavable GFLG tetrapeptide
t½:
5.72 h
SASA supp.
82.5%
Efficacy
101.1%
Late/Early
5.58×
Score
0.7844
MW (est.)
5838 Da

Activation Profile

0%25%50%75%100%0h0.5h1h2h4h8h12h24hBaseline GLP-1Glyco-masked

Near-identical profile to Rank 1 but without the G28A cap mutation. Slightly higher MW; serves as synthetic control to isolate G28A contribution.

Rank 3GLP1-GM-E562AD
View in Mol*

Sequence & Mutations

HTEGTFTSDVSAYLQGQAAIEFIAWLVKGR
  • A8TO-glycosylation anchor
  • S18AHelix stabilisation
  • E21QNeutral amide
  • L26IConservative Leu→Ile; branched chain maintains hydrophobicity

Design

Glycan:
Biantennary sialylated N-glycan
Position:
Glu9 (O-linked via A8T→Thr anchor)
Linker:
Cathepsin B-cleavable GFLG tetrapeptide
t½:
5.72 h
SASA supp.
82.5%
Efficacy
92.8%
Late/Early
5.58×
Score
0.7472
MW (est.)
5708 Da

Activation Profile

0%25%50%75%100%0h0.5h1h2h4h8h12h24hBaseline GLP-1Glyco-masked

Lower efficacy (92.8%) due to absence of Y25W gain; L26I conservative change has minimal effect. Useful as a lower-efficacy control to validate the nausea-reduction hypothesis independently of receptor activation.

Comparison vs Baseline GLP-1

MoleculeSASA suppressionEarly activation (0–2 h)Late activation (2–24 h)Late/Early ratioNausea risk
Baseline GLP-10%~95%~90%1.05HIGH
GLP1-GM-F54D5482.5%~49% at 2 h~67% at 4 h5.58×LOW
GLP1-GM-94230382.5%~49% at 2 h~67% at 4 h5.58×LOW
GLP1-GM-E562AD82.5%~49% at 2 h~67% at 4 h5.58×LOW
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